issue with this wf in command-line environment #11
Description
Will this workflow work in the command-line environment? Or is it supposed for EPI2ME only?
After I pulled it from github with this command nextflow pull artic-network/squirrel-nf, I ran this command nextflow run artic-network/squirrel-nf --help. It throwed me the following error.
Command error:
/opt/conda/lib/python3.11/site-packages/squirrel/utils/initialising.py:5: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
import pkg_resources
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 1 (use --cores to define parallelism)
Rules claiming more threads will be scaled down.
Job stats:
job count
align_to_reference 1
all 1
mask_repetitive_regions 1
total 3
Select jobs to execute...
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 1 (use --cores to define parallelism)
Rules claiming more threads will be scaled down.
Select jobs to execute...
/opt/conda/lib/python3.11/site-packages/stopit/init.py:10: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
import pkg_resources
cat: null: Is a directory
[Fri Aug 15 12:43:01 2025]
Error in rule align_to_reference:
jobid: 0
input: null, /opt/conda/lib/python3.11/site-packages/squirrel/data/NC_063383.fasta
output: squirrel_tmp/tmpga4ftskf/msa.fasta
log: squirrel_tmp/tmpga4ftskf/logs/minimap2_sam.log (check log file(s) for error details)
RuleException:
CalledProcessError in file /opt/conda/lib/python3.11/site-packages/squirrel/scripts/msa.smk, line 49:
Command 'set -euo pipefail; cat "null" | awk '{ if ($0 !~ /^>/) { gsub("-", "",$0); } print $0; }' | awk '{ { gsub(" ", "",$0); } { gsub(",", "",$0); } print $0; }' | minimap2 -a -x asm20 -rmq=no --junc-bonus=0 --for-only --sam-hit-only --secondary=no --score-N=0 -t 1 /opt/conda/lib/python3.11/site-packages/squirrel/data/NC_063383.fasta - -o squirrel_tmp/tmpga4ftskf/mapped.sam &> squirrel_tmp/tmpga4ftskf/logs/minimap2_sam.log
gofasta sam toMultiAlign -s squirrel_tmp/tmpga4ftskf/mapped.sam -t 1 --reference /opt/conda/lib/python3.11/site-packages/squirrel/data/NC_063383.fasta --trimstart 0 --trimend 190788 --trim --pad -o 'squirrel_tmp/tmpga4ftskf/msa.fasta' &> squirrel_tmp/tmpga4ftskf/logs/minimap2_sam.log' returned non-zero exit status 1.
File "/opt/conda/lib/python3.11/site-packages/squirrel/scripts/msa.smk", line 49, in __rule_align_to_reference
File "/opt/conda/lib/python3.11/concurrent/futures/thread.py", line 58, in run
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2025-08-15T124300.590332.snakemake.log
Query file: null
Work dir:
/home/odin-ml/work/a1/7edc2eec968308712a4f739ea5aa77
Container:
community.wave.seqera.io/library/squirrel:1.1.5--b41340e6d2ba2b30
Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out
-- Check '.nextflow.log' file for details